Benjamin Mark Lewis

San Diego, California

I am a biological data scientist, with a strong wet lab prior. For over a decade, I have operated at the interface of computational and experimental biology, integrating multiomic datasets with functional assays to extract mechanism, de-risk hypotheses, and accelerate therapeutic discovery.

My foundation in cell and molecular biology informs rigorous experimental design, scalable analytical strategy, and clear cross-functional execution across dry and wet lab teams. I focus on translating high-dimensional data into decisive biological insight.

My publications in RNA and Cell Reports span RNA binding protein biology in mitochondrial regulation, CRISPR-based gene correction in iPSC disease models, and cell therapy approaches for hemophilia.

news

Jan 01, 2026	Ben promoted to Senior Scientist, Bioinformatics at Actio Biosciences in recognition of scientific leadership, cross-program impact, and strategic contributions to portfolio advancement.
Sep 01, 2024	Ben becomes a dad.
Apr 01, 2024	Benjamin Mark Lewis joins Actio Biosciences as a Bioinformatics Scientist II.
Apr 25, 2022	Benjamin Mark Lewis joins Aspen Neuroscience as a Scientist in Research and Development.
Mar 14, 2022	Benjamin Mark Lewis, PhD, Successfully Completes Thesis Defense in Molecular Biology at University of California, San Diego, in the Labs of Gene Yeo and Tony Hunter

latest posts

Jan 03, 2025	a hello word post

selected publications

Functional Gene Correction for Cystic Fibrosis in Lung Epithelial Cells Generated from Patient iPSCs

Amy L. Firth, Tushar Menon, Gregory S. Parker, and 8 more authors

Cell Reports, Sep 2015

Abs DOI

Lung disease is a major cause of death in the United States, with current therapeutic approaches serving only to manage symptoms. The most common chronic and life-threatening genetic disease of the lung is cystic fibrosis (CF) caused by mutations in the cystic fibrosis transmembrane regulator (CFTR). We have generated induced pluripotent stem cells (iPSCs) from CF patients carrying a homozygous deletion of F508 in the CFTR gene, which results in defective processing of CFTR to the cell membrane. This mutation was precisely corrected using CRISPR to target corrective sequences to the endogenous CFTR genomic locus, in combination with a completely excisable selection system, which significantly improved the efficiency of this correction. The corrected iPSCs were subsequently differentiated to mature airway epithelial cells where recovery of normal CFTR expression and function was demonstrated. This isogenic iPSC-based model system for CF could be adapted for the development of new therapeutic approaches.
Autologous and Heterologous Cell Therapy for Hemophilia B toward Functional Restoration of Factor IX

Suvasini Ramaswamy, Nina Tonnu, Tushar Menon, and 5 more authors

Cell Reports, May 2018

Abs DOI

Hemophilia B is an ideal target for gene- and cell-based therapies because of its monogenic nature and broad therapeutic index. Here, we demonstrate the use of cell therapy as a potential long-term cure for hemophilia B in our FIX-deficient mouse model. We show that transplanted, cryopreserved, cadaveric human hepatocytes remain functional for more than a year and secrete FIX at therapeutic levels. Hepatocytes from different sources (companies and donors) perform comparably in curing the bleeding defect. We also generated induced pluripotent stem cells (iPSCs) from two hemophilia B patients and corrected the disease-causing mutations in them by two different approaches (mutation specific and universal). These corrected iPSCs were differentiated into hepatocyte-like cells (HLCs) and transplanted into hemophilic mice. We demonstrate these iPSC-HLCs to be viable and functional in mouse models for 9–12 months. This study aims to establish the use of cells from autologous and heterologous sources to treat hemophilia B.
LARP4 is an RNA-binding protein that binds nuclear-encoded mitochondrial mRNAs to promote mitochondrial function

Benjamin M. Lewis, Chae Yun Cho, Hsuan-Lin Her, and 3 more authors

RNA, Feb 2024

Abs DOI

Mitochondria-associated RNA-binding proteins (RBPs) have emerged as key contributors to mitochondrial biogenesis and homeostasis. With few examples known, we set out to identify RBPs that regulate nuclear-encoded mitochondrial mRNAs (NEMmRNAs). Our systematic analysis of RNA targets of 150 RBPs identified RBPs with a preference for binding NEMmRNAs, including LARP4, a La RBP family member. We show that LARP4’s targets are particularly enriched in mRNAs that encode respiratory chain complex proteins (RCCPs) and mitochondrial ribosome proteins (MRPs) across multiple human cell lines. Through quantitative proteomics, we demonstrate that depletion of LARP4 leads to a significant reduction in RCCP and MRP protein levels. Furthermore, we show that LARP4 depletion reduces mitochondrial function, and that LARP4 re-expression rescues this phenotype. Our findings shed light on a novel function for LARP4 as an RBP that binds to and positively regulates NEMmRNAs to promote mitochondrial respiratory function.